4G92

CCAAT-binding complex from Aspergillus nidulans with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

DNA Minor Groove Sensing and Widening by the CCAAT-Binding Complex.

Huber, E.M.Scharf, D.H.Hortschansky, P.Groll, M.Brakhage, A.A.

(2012) Structure 20: 1757-1768

  • DOI: 10.1016/j.str.2012.07.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The CCAAT box is a frequent element of eukaryotic promoters, and its specific recognition by the conserved heterotrimeric CCAAT-binding complex (CBC) constitutes a key step in promoter organization and regulation of transcription. Here, we report the ...

    The CCAAT box is a frequent element of eukaryotic promoters, and its specific recognition by the conserved heterotrimeric CCAAT-binding complex (CBC) constitutes a key step in promoter organization and regulation of transcription. Here, we report the crystal structures of the CBC from Aspergillus nidulans in the absence and in complex with double-stranded DNA at 1.8 Å resolution. The histone-like subunits HapC and HapE induce nucleosome-like DNA bending by interacting with the sugar-phosphate backbone. Minor groove sensing and widening by subunit HapB tightly anchor the CBC to the CCAAT box, as shown by structural and biochemical data. Furthermore, crucial interactions of the DNA duplex with subunit HapB provide an explanation for the sequence specificity of the CBC. The herein-described mode of transcription factor binding answers the question of how histone proteins gained sequence specificity for the CCAAT box.


    Organizational Affiliation

    Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Garching 85747, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HAPB protein
A
64Emericella nidulansMutation(s): 0 
Gene Names: hapB
Find proteins for P87249 (Emericella nidulans)
Go to UniProtKB:  P87249
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Transcription factor HapC (Eurofung)
B
92Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139)Mutation(s): 0 
Find proteins for Q5B5Z6 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139))
Go to UniProtKB:  Q5B5Z6
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HapE
C
119Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139)Mutation(s): 0 
Find proteins for C8V0B5 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139))
Go to UniProtKB:  C8V0B5
Entity ID: 4
MoleculeChainsLengthOrganism
DNAD25N/A
Entity ID: 5
MoleculeChainsLengthOrganism
DNAE25N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.157 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.040α = 90.00
b = 72.890β = 90.00
c = 145.890γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata scaling
XDSdata reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-31
    Type: Initial release